Simulation of the effects of Si/Al ratio (material variable) and pressure (operational variable) on water purification with zeolite membranes was discussed. LTA, FAU, and MFI zeolitic structures, respectively having low (1.5), medium (5.6), and high (15) Si/Al ratio were created in Packmol software followed by determining their parameters in LAMMPS varying pressure (12, 24, 36, and 48 MPa). Lenard-Jones interactions were considered applying Tersoff hybrid force field with water modeling based on TIP3P and CHARMM force field. Typical pollutants representing different electronegativity (2.19 for Pb2+ and 1.88 for Co2+) along with chlorine ions (Cl−) were subjected to dynamic simulation for 0.5 ns of equilibrium. Water and ions flux passing the membranes both increase upon pressure rise, particularly at a low Si/Al ratio. Moreover, van der Waals, mean square displacement (MSD), and ion density were captured. Graphical illustrations unveiled dominant mechanisms by VMD software. MFI membrane with rejection above 80% was the bests membrane. The LTA membrane's water flux was the highest, with ca. 3000 ns−1 passing water molecules. van der Waals patterns suggest heavy metal ions trapped in zeolite and their accumulation and agglomeration behind the membrane.